phenoData {Biobase}R Documentation

Class For Patient or Experiment Level Data

Description

The class consists of a data.frame and some accompanying methods suited to handle patient level data for microarrays.

Creating Objects

new('phenoData', pData = [data.frame], varLabels = [list], varMetadata = [data.frame])

Slots

pData:
Object of class 'data.frame'. The data.
varLabels:
Object of class 'list'. Obtional long labels for the different variables.
varMetadata:
Object of class 'data.frame'. A data frame with a column named varNames and arbitrarily many additional columns.

Methods

Class-specific methods:

addVarMetadataEntry(phenoData, character, character, ANY)
Not documented: FIXME: it should be a replace method, otherwise it is not clear how should it work
combine(phenoData, phenoData)
Combines several instances into a single 'phenoData' instance. See combine
convertVarLabels(phenoData)
Not documented
getVarMetadata(phenoData, character, character) or getVarMetadata(phenoData, character, missing)
Not documented
getUnits(phenoData, character
Not documented
pData(phenoData), pData(phenoData)<-
Get/set methods for slot pData
phenoData(exprSet)<-
A replacement method for the phenoData slot
split(phenoData, vector)
FIXME: there is no implementation!!! A method to split pData and return a list of phenoData objects. Unlike split this function requires the number of rows of pData to be a multiple of the length of vector
varLabels(phenoData)
A method to display the variable labels.
varMetadata(phenoData)
Not documented

Standard methods defined for 'phenoData':

$(name), $(name, value)<-
An old-style method to get and set. It is pData(object)[[as.character(val)]] which does not quite have the right semantics but it is close. This operator extracts the named component of the pData slot in phenoData.
[(phenoData)
A subset operator
[[(phenoData), [[(phenoData)<-
A get/set subset operator
show(phenoData)
Displays the data in a readable manner

Functions defined in Biobase to operate with 'phenoData' instances include:

df2pD(x, varLabels, varMetadata)
Function to coerce from a data.frame to a phenoData object. Here x is the data.frame to be coerced; varLabels is a character describing each of the columns in x and varMetadata is a more extensive descriptions of the variables in x, including units of measurement etc
read.phenoData
See help on read.phenoData

See Also

read.phenoData, combine

Examples

data(eset)
pes <- phenoData(eset)
pes <- convertVarLabels(pes)
varMetadata(pes)
pes <- addVarMetadataEntry(pes, "cov1", "units", "inches")
getUnits(pes, "cov1")

   # example for 'df2pD'
   data(cars)
   d1 = df2pD(cars)

[Package Biobase version 1.8.0 Index]